Question regarding syncing books from computer to ipad

I am fairly new to the Apple ecosystem (wife has had an iphone for awhile but I just got an ipad mini and just installed itunes on my PC.)

I have figured out how to sync music using imatch and can see my whole music collection on the ipad. Pretty slick.

However I can't figure out books. I have a lot of ebooks not purchased in itunes. I have pointed my PC itunes library at the ebook folder and can see all the books in itunes on my PC.

However I don't see them on my ipad in iTunes or iBooks. I assumed they should show up as I am using the same iTunes account on the PC and the ipad?

In case this is relevant, I have iCloud activated on my ipad, but it is a different Apple ID than iTunes (the iTunes account is my wife's email and that email is associated with her icloud on her iphone).